merge two text file without common column in python

Question

I have 2 text files with the same number of rows, but there is no common column between my files. the first file has 9 columns and the 2nd one has 8 columns. both of them have 111557 rows. the order of rows in 2 files is the same, so I just want to simply merge them, which means I would have one text file with 17 columns.

This is the first column of the 1st .txt file (they are tab limited)

     chr1   HAVANA  gene    29554   31109   .   +   .

This is the 1st line of the 2nd .txt file(they are tab limited)

     ENSG00000243485.2  ENSG00000243485.2   lincRNA NOVEL   MIR1302-11  lincRNA NOVEL   MIR1302-11

Please post one line from each file, and the corresponding desired line in the output file. What are the columns separated by? — inspectorG4dget
– inspectorG4dget, Commented Dec 30, 2014 at 20:28
Ok, this is just too much. Did you try to google anything? Do you have any of your own code? Even a line to open a file? To read lines from the file? To write a line to a file? When you have those, we can talk. — bosnjak
– bosnjak, Commented Dec 30, 2014 at 20:31

inspectorG4dget · Accepted Answer · 2014-12-30 20:45:06Z

3

import csv

with open('path/to/file1') as infile1, open('path/to/file2') as infile2, open('path/to/output', 'w') as outfile:
    writer = csv.writer(outfile, delimiter='\t')
    for row1,row2 in zip(csv.reader(infile1, delimiter='\t'), csv.reader(infile2, delimiter='\t')):
        writer.writerow(row1+row2)

edited Dec 30, 2014 at 20:45

answered Dec 30, 2014 at 20:34

inspectorG4dget

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2 Comments

inspectorG4dget Over a year ago

@ali: this is exactly why I posted a comment for clarification on your original post. Please address that, without which I can't provide a super-accurate answer

inspectorG4dget Over a year ago

@ali: I've updated my answer to be exactly what you need

Hackaholic · Accepted Answer · 2014-12-30 21:07:34Z

2

try like this:

with open('file1') as f1, open('file2') as f2, open('outfile','w') as out:
    for x in f1:
        y = next(f2)
        out.write("{}\t{}".format(x.strip(),y))

try like this if you getting error in above:

f1 = open('file1') 
f2 = open('file2')
out = open('outfile','w')
for x in f1:
    y = next(f2)
    out.write(x.strip() + "\t" + y)

edited Dec 30, 2014 at 21:07

answered Dec 30, 2014 at 20:41

Hackaholic

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5 Comments

inspectorG4dget Over a year ago

I like it, but this only works if OP's files are space delimited, which is similar to the assumption I made. The question really isn't super clear

ali Over a year ago

@ Hackaholic my files are tab limited

ali Over a year ago

gives this error: SyntaxError: invalid syntax and it is related to "," after f1

ali Over a year ago

with open('fisrts.txt') as f1, open('eights.txt') as f2, open('outfile.txt','w') as out: ^ SyntaxError: invalid syntax

Hackaholic Over a year ago

@ali check the next version of solution

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